This invention relates to the formation and dissolution of double stranded nucleic acid molecules and to the interactions between double and single stranded nucleic acid molecules and nucleic acid-binding ligands. For example it relates to: DNA sequence design and construction including, e.g., methods for determining and preparing DNA sequences with selected reaction attributes, such as binding affinities for their respective ligands; and the use of such sequences in diagnostic or analytical procedures to detect target DNA, e.g., viral DNA.